To describe the epidemiological and genomic profile of COVID-19 during the 4th epidemic wave in Mauritania.This is a cross-sectional study in Mauritania, from October 1, 2021, to February 28, 2022. Were included all people in the process of travel, performing an RT-PCR, at the level of the National Research Institute in Public Health and patients who have been sampled for sequencing by teams from the Department of Strategic Information and Epidemiological Surveillance.Out of 37,574 RT-PCR tests collected on March 3, 2022, during the study period, 1,465 cases were diagnosed positive for COVID-19 (3.9%), with an average age of 39±14,6 years and a sex ratio of 2.08. Of the 112 genomic sequences performed, 75 were of the Omicron variant (66.9%). The average age was 40±15 years, with extremes of 15 to 82 years and a sex ratio of 0.97. The vaccination status was assured in 67.7% of patients and the peak of the Omicron variant was reached during the first week of January 2022.The Omicron variant was predominant during the 4th wave in Mauritania. As part of its response plan against COVID-19, the installation of new sequencing units inside the country and the strengthening of the training of technicians in the virology laboratory will be essential. 

Characterization of a cluster of COVID-19 cases linked to the Omicron variant, in Mauritania.

•Omicron variant continues to progress in Senegal with the appearance of new contaminations.•IRESSEF detected the first positive case of the Omicron variant on Friday, December 3, 2021.•Since this date, the number of Omicron variant infections has increased over the weeks.•Molecular surveillance of the Omicron variant allowed us to identify a strong variation of this variant in our country. 

https://doi.org/10.1016/j.nmni.2022.100990

Heterogeneity of the Omicron variant in Senegal

Résumé Objectif: Décrire le profil épidémiologique et génomique de la COVID-19 au cours de la 4ème vague épidémique, en Mauritanie. Méthodes: Il s’agissait d’une étude transversale en Mauritanie, du 1eroctobre 2021 au 28 février 2022. Ont été incluses toutes les personnes en instance de voyage, réalisant un RT-PCR, au niveau de l’Institut National de Recherche en Santé Publique (INRSP) et les patients ayant été prélevés, pour séquençage, par les équipes de la Direction de l’Information Stratégique et de la Surveillance Epidémiologique du Ministère de la Santé en Mauritanie. Résultats: Sur 37574 tests RT-PCR, colligés le 3 Mars 2022 durant la période d’étude, 1465 cas ont été diagnostiqués positifs à la COVID-19 (3,9%), avec une moyenne d’âge de 39±14,6 ans et un sex-ratio de 2,08. Sur les 112 séquençages génomiques réalisés, 75 ont été du variant Omicron (66,9%). L’âge moyen de ces patients a été de 40±15 ans, avec des extrêmes de 15 à 82 ans et un sex-ratio de 0,97. L’état vaccinal a été assuré chez 67,7% des patients et le pic du variant Omicron a été atteint durant la première semaine du mois de janvier 2022. Conclusion: Le variant Omicron a été prédominant au cours de la 4èmevague de l’épidémie COVID-19 en Mauritanie. Dans le cadre de son plan de riposte, l’installation de nouvelles unités de séquençage de la COVID-19 à l’intérieur du pays et le renforcement de la formation des techniciens en laboratoire de virologie, seront actuellement indispensables.

Caractérisation d’un cluster des cas de COVID-19 liés au variant Omicron, en Mauritanie

The rapid genetic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the coronavirus disease 2019 (COVID-19) pandemic has greatly challenged public health authorities worldwide, including in Mauritania. Despite the presence of the virus in Mauritania, only one study described its genomic variation during the course of the epidemic. The purpose of the present study was to document the genomic pattern of SARS-CoV-2 variants from clinical isolates during the COVID-19 outbreak in Mauritania, from September to November 2021. The whole genomes from 54 SARS-CoV-2 strains detected in nasopharyngeal swabs with a cycle threshold value ≤ 30 were successfully sequenced using next-generation sequencing (NGS) and the Illumina protocol. The mean genome coverage (±standard deviation) was 96.8% (±3.7). The most commonly identified clade was 21J (57.4%), followed by 21D (16.7%), 20A (11.1%), and 20B (9.2%). At the level of lineages, the majority of the samples were Delta variants with the sub-lineage AY.34 (or B.1.617.2.34). Among the 54 SARS-CoV-2 isolates that were successfully sequenced, 33 (61.1%) came from vaccinated individuals, and 21 (38.9%) were from unvaccinated individuals. Several SARS-CoV-2 variants were present in Mauritania between September and November 2021. As Mauritania, like many West African countries, is resource-limited regarding viral genome sequencing facilities, establishment of mutualized sub-regional sequencing platforms will be necessary to ensure continuous monitoring of mutations in viral genomes and track potential reduction in COVID-19 vaccine efficacy, increased transmissibility, and disease severity.

Genomic Characterization of SARS-CoV-2 Variants from Clinical Isolates during the COVID-19 Epidemic in Mauritania

Initially reported to the World Health Organization (WHO) on November, 24th, 2021, the patient self-reporting and medical reporting of symptoms unique to SARS-CoV-2 (B.1.1.529; Omicron variant) has differed from that of other mutants. A notable symptom has been lower back pain, which sets the variant apart from others (which originated before and after). B.1.1.529 remains a threat in communities across the world, and this analytical study emphasizes the importance of symptom awareness in the ongoing pandemic. 

Elevated Catabolic Symptoms Characteristic in Lumbar Region Prevalent with B.1.1.529 Patients and Correlation with Localized Reactions in Comparable Illnesses

•Omicron variant continues to progress in Senegal with the appearance of new contaminations.•IRESSEF detected the first positive case of the Omicron variant on Friday, December 3, 2021.•Since this date, the number of Omicron variant infections has increased over the weeks.•Molecular surveillance of the Omicron variant is carried out in real time to inform the medical authorities. 

https://doi.org/10.1016/j.nmni.2022.100959

Rapidly rising cases with Omicron in Senegal

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Rapidly rising cases with Omicron in Senegal